[2024-01-24 12:31:03,634] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:03,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:03,639] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b60a9c8-45ef-4d9b-b299-45214e792fca/dqc_reference
[2024-01-24 12:31:04,924] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:04,924] [INFO] Task started: Prodigal
[2024-01-24 12:31:04,925] [INFO] Running command: gunzip -c /var/lib/cwl/stg8bb68311-b817-4e2a-91be-f2b0d8347fb1/GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/cds.fna -a GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:25,516] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:25,517] [INFO] Task started: HMMsearch
[2024-01-24 12:31:25,517] [INFO] Running command: hmmsearch --tblout GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b60a9c8-45ef-4d9b-b299-45214e792fca/dqc_reference/reference_markers.hmm GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:25,849] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:25,850] [INFO] Found 6/6 markers.
[2024-01-24 12:31:25,890] [INFO] Query marker FASTA was written to GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:31:25,891] [INFO] Task started: Blastn
[2024-01-24 12:31:25,891] [INFO] Running command: blastn -query GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b60a9c8-45ef-4d9b-b299-45214e792fca/dqc_reference/reference_markers.fasta -out GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:26,489] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:26,494] [INFO] Selected 15 target genomes.
[2024-01-24 12:31:26,495] [INFO] Target genome list was writen to GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:31:26,510] [INFO] Task started: fastANI
[2024-01-24 12:31:26,510] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bb68311-b817-4e2a-91be-f2b0d8347fb1/GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna.gz --refList GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:39,025] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:39,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b60a9c8-45ef-4d9b-b299-45214e792fca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:39,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b60a9c8-45ef-4d9b-b299-45214e792fca/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:39,038] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:31:39,038] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:31:39,039] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Algoriphagus hitonicola	strain=DSM 19315	GCA_900113375.1	435880	435880	type	True	100.0	1420	1424	95	conclusive
Algoriphagus faecimaris	strain=DSM 23095	GCA_900101705.1	686796	686796	type	True	80.9206	766	1424	95	below_threshold
Algoriphagus faecimaris	strain=JCM 16561	GCA_002150585.1	686796	686796	type	True	80.8914	777	1424	95	below_threshold
Algoriphagus algorifonticola	strain=hg1	GCA_007655305.1	2593007	2593007	type	True	78.0316	371	1424	95	below_threshold
Algoriphagus ornithinivorans	strain=DSM 15282	GCA_900115305.1	226506	226506	type	True	78.0139	355	1424	95	below_threshold
Algoriphagus vanfongensis	strain=DSM 17529	GCA_000429465.1	426371	426371	type	True	77.762	279	1424	95	below_threshold
Algoriphagus aquimaris	strain=F21	GCA_004358035.1	2547398	2547398	type	True	77.7598	328	1424	95	below_threshold
Algoriphagus formosus	strain=XAY3209	GCA_002807035.1	2007308	2007308	type	True	77.6829	338	1424	95	below_threshold
Algoriphagus boritolerans	strain=DSM 17298	GCA_900108085.1	308111	308111	type	True	77.4881	266	1424	95	below_threshold
Algoriphagus iocasae	strain=DSM 102044	GCA_014206875.1	1836499	1836499	type	True	77.4739	214	1424	95	below_threshold
Algoriphagus mannitolivorans	strain=DSM 15301	GCA_000429425.1	226504	226504	type	True	77.3673	237	1424	95	below_threshold
Algoriphagus aquaeductus	strain=T4	GCA_003253485.1	475299	475299	type	True	77.2257	281	1424	95	below_threshold
Algoriphagus lacus	strain=N3	GCA_003583985.1	2056311	2056311	type	True	77.1576	253	1424	95	below_threshold
Algoriphagus alkaliphilus	strain=DSM 22703	GCA_900103735.1	279824	279824	type	True	76.9636	253	1424	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:39,040] [INFO] DFAST Taxonomy check result was written to GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:31:39,041] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:39,041] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:39,041] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b60a9c8-45ef-4d9b-b299-45214e792fca/dqc_reference/checkm_data
[2024-01-24 12:31:39,042] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:39,084] [INFO] Task started: CheckM
[2024-01-24 12:31:39,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/checkm_input GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:32:40,036] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:40,038] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:40,063] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:40,064] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:40,064] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:32:40,064] [INFO] Task started: Blastn
[2024-01-24 12:32:40,065] [INFO] Running command: blastn -query GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b60a9c8-45ef-4d9b-b299-45214e792fca/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:40,923] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:40,928] [INFO] Selected 18 target genomes.
[2024-01-24 12:32:40,928] [INFO] Target genome list was writen to GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:40,940] [INFO] Task started: fastANI
[2024-01-24 12:32:40,941] [INFO] Running command: fastANI --query /var/lib/cwl/stg8bb68311-b817-4e2a-91be-f2b0d8347fb1/GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna.gz --refList GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:55,398] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:55,420] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:55,420] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_900113375.1	s__Algoriphagus hitonicola	100.0	1420	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900101705.1	s__Algoriphagus faecimaris	80.8951	770	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	0.98	0.98	2	-
GCF_000526355.1	s__Algoriphagus marincola_A	78.0554	355	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007655305.1	s__Algoriphagus sp007655305	78.0312	371	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115305.1	s__Algoriphagus ornithinivorans	78.0101	356	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	95.91	95.63	0.88	0.85	7	-
GCF_000429465.1	s__Algoriphagus vanfongensis	77.762	279	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002807035.1	s__Algoriphagus formosus	77.6805	337	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	97.55	97.55	0.93	0.93	2	-
GCF_900108085.1	s__Algoriphagus boritolerans	77.4851	267	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.80	99.80	0.99	0.99	2	-
GCF_014206875.1	s__Algoriphagus iocasae	77.4691	213	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429425.1	s__Algoriphagus mannitolivorans	77.3673	237	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571135.1	s__Algoriphagus kandeliae	77.3539	320	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003259255.1	s__Algoriphagus litoralis	77.2603	242	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253485.1	s__Algoriphagus aquaeductus	77.2275	280	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003583985.1	s__Algoriphagus lacus	77.1686	252	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116615.1	s__Algoriphagus locisalis	77.0836	196	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103735.1	s__Algoriphagus alkaliphilus	76.9929	251	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	99.41	99.41	0.93	0.93	2	-
GCF_002002735.1	s__Algoriphagus sp002002735	76.8732	241	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014838715.1	s__Algoriphagus sp014838715	76.8521	192	1424	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Cyclobacteriaceae;g__Algoriphagus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:55,423] [INFO] GTDB search result was written to GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:55,423] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:55,430] [INFO] DFAST_QC result json was written to GCF_900113375.1_IMG-taxon_2622736517_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:32:55,430] [INFO] DFAST_QC completed!
[2024-01-24 12:32:55,431] [INFO] Total running time: 0h1m52s